SASDC45: Alpha domain of autotransporter protein UpaB from UPEC

Basic information

• Entry: Database: SASBDB / ID: SASDC45

Sample

Alpha domain of autotransporter protein UpaB from UPEC

• Alpha domain of autotransporter protein UpaB (protein), Alpha-UpaB, E. Coli CFT073

Function / homology

Function:

outer membrane

Domain/homology:

Pertactin virulence factor family / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor

Component:

Autotransporter domain-containing protein

• Biological species: E. Coli CFT073
• Citation: Journal: Nat Commun / Year: 2019; Title: Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules.; Authors: Jason J Paxman / Alvin W Lo / Matthew J Sullivan / Santosh Panjikar / Michael Kuiper / Andrew E Whitten / Geqing Wang / Chi-Hao Luan / Danilo G Moriel / Lendl Tan / Kate M Peters / Minh-Duy Phan / Christine L Gee / Glen C Ulett / Mark A Schembri / Begoña Heras / ; Abstract: Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation of host epithelial surfaces. Here we present the crystal structure of UpaB, an autotransporter that is known to contribute to uropathogenic E. coli (UPEC) colonisation of the urinary tract. We provide evidence that UpaB can interact with glycosaminoglycans and host fibronectin. Unique modifications to its core β-helical structure create a groove on one side of the protein for interaction with glycosaminoglycans, while the opposite face can bind fibronectin. Our findings reveal far greater diversity in the autotransporter β-helix than previously thought, and suggest that this domain can interact with host macromolecules. The relevance of these interactions during infection remains unclear.

Contact author

• Andrew Whitten (ANSTO, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW 2232, Australia)

Models

• Model #1327: ; Type: dummy / Software: (2.8.0) / Radius of dummy atoms: 2.50 A / Symmetry: P1 / Chi-square value: 1.468 / P-value: 0.021000; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1328: ; Type: mix / Software: (1.1) / Radius of dummy atoms: 1.90 A / Symmetry: P1; Comment: Coral was used to model residues from the N-terminus and C-terminus missing from the PDB model; Chi-square value: 1.77; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Alpha domain of autotransporter protein UpaB from UPEC; Specimen concentration: 0.10-2.70
• Buffer: Name: 25 mM HEPES 150 mM NaCl / pH: 7

Entity #708

Name: Alpha-UpaB / Type: protein / Description: Alpha domain of autotransporter protein UpaB / Formula weight: 47.673 / Num. of mol.: 1 / Source: E. Coli CFT073 / References: UniProt: A0A0H2V5A3
Sequence:

SNATDSTVST DPVTLNTEKT TLDQDVVING DNKITAVTIE TSDSDKDLNV TFGGHDITAA STVNQDFVEG VKVSGNKNVV INATDSTITA QGEGTYVRTA MVIDSTGDVV VNGGNFVAKN EKGSATGISL EATTGNNLTL NGTTINAQGN KSYSNGSTAI FAQKGNLLQG FDGDATDNIT LADSNIINGG IETIVTAGNK TGIHTVNLNI KDGSVIGAAN NKQTIYASAS AQGAGSATQN LNLSVADSTI YSDVLALSES ENSASTTTNV NMNVARSYWE GNAYTFNSGD KAGSDLDINL SDSSVWKGKV SGAGDASVSL QNGSVWNVTG SSTVDALAVK DSTVNITKAT VNTGTFASQN GTLIVDASSE NTLDISGKAS GDLRVYSAGS LDLINEQTAF ISTGKDSTLK ATGTTEGGLY QYDLTQGADG NFYFVKNTHK ASNASSVIQA MAAAPANVAN LQADTL

Experimental information

• Beam: Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 1.428 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Alpha domain of autotransporter protein UpaB from UPEC
Measurement date: May 1, 2015 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 35 / Unit: 1/A /

	Min	Max
Q	0.0114	0.2998

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 396 /

	Min	Max
Q	0.01136	0.2998
P(R) point	1	396
R	0	105

Result

Type of curve: single_conc

	Experimental	Standard	Standard error	Porod
MW	46.7 kDa	46.7 kDa	2.5	54.1 kDa
Volume	-	-	-	66 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.0271	5.0E-5	0.0271	6.0E-5
Radius of gyration, Rg	2.97 nm	0.01	2.93 nm	0.01

	Min	Max	Error
D	-	10.5	0.5
Guinier point	1	41	-